Could a non-exclusive author upload the same track to multiple sites and receive royalties only from the ones that support PRO-registered music?
Yes
Aside from the author not getting royalties, could this situation create a problem for any of the parties involved? For example, would either Production Company A or Broadcast Station B be penalized in any way?
Probably not, as if a cue sheet is not filled in the monies will go into an uncollected pool.
Is it possible that a YouTube video could get taken down or the music removed?
I would love to see an update on this subject. Great insights 
Two observations Iāve made in the past couple of months:
Iāve had this issue that my free file has been aired on national television and radio several times - without a purchase of the right license. Iāve also had two tracks on my non-RF soundcloud profile which have been downloaded by mainly radio stations. It seems that these stations actively search for what they call ācompletely free musicā. Iāve disabled the download by now and Iād advise you to do the same.
To get things straight. We as musicians choose to join a PRO, so we can protect the right of our music. And I bet, everyone who considers himself/herself a serious musician/composer/songwriter/performer knows this and he or she is member of a PRO. Envato (refusing to allow PRO registering here on AJ) is degrading his Authors to non-professionals. You could argue with ādonāt find this marketplace fair? look elsewhereā, but this isnāt working here, because of Envatos huge popularity.
Not sure, but I think youāll find that itās not a question of Envato allowing PRO registration of tracks, but more to do with the Royalty Free aspect. For example, Iām pretty sure the PRS does not allow RF tracks to be registered on its books. In fact, if anyone was caught registering RF tracks with them, they would take a pretty dim view of it and you could very easily being banned.
Royalty Free and Rights Managed tracks are separate issues.
Any news on that? I have like 40 tracks I could put here but they are registered with a PRO (SGAE)
I got a note saying āpost canāt be emptyā so I deleted my post
Just in case people donāt know yet, AJ now ALLOWS PRO-registered music! This is the greatest thing Envato did for Audiojungle, and frankly the only reason why Iām back and ready to upload music again. Rock n roll!